Source code for immuneML.encodings.DatasetEncoder

import abc
import pickle
import shutil
from pathlib import Path
from typing import List

from immuneML.IO.dataset_export.ImmuneMLExporter import ImmuneMLExporter
from immuneML.encodings.EncoderParams import EncoderParams

[docs] class DatasetEncoder(metaclass=abc.ABCMeta): """ YAML specification: encodings: e1: <encoder_class> # encoding without parameters e2: <encoder_class>: # encoding with parameters parameter: value """
[docs] @staticmethod @abc.abstractmethod def build_object(dataset, **params): pass
[docs] @abc.abstractmethod def encode(self, dataset, params: EncoderParams): pass
[docs] @staticmethod def load_encoder(encoder_file: Path): with"rb") as file: encoder = pickle.load(file) return encoder
[docs] @staticmethod def load_attribute(encoder, encoder_file: Path, attribute: str): if encoder_file is not None: file_path = encoder_file.parent / getattr(encoder, attribute).name setattr(encoder, attribute, file_path) assert getattr(encoder, attribute).is_file(), f"{type(encoder).__name__}: could not load {attribute} from {getattr(encoder, attribute)}." return encoder
[docs] @staticmethod def store_encoder(encoder, encoder_file: Path): with"wb") as file: pickle.dump(encoder, file) encoder_dir = encoder_file.parent for file in encoder.get_additional_files(): shutil.copy(file, encoder_dir / return encoder_file
[docs] @staticmethod def get_additional_files() -> List[str]: '''Should return a list with all the files that need to be stored when storing the encoder.''' return []
[docs] def set_context(self, context: dict): return self
[docs] def store(self, encoded_dataset, params: EncoderParams): ImmuneMLExporter.export(encoded_dataset, params.result_path)